IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS, VOL. 25, NO. 2, FEBRUARY 2006 211 Microfluidics-Based Biochips: Technology Issues, Implementation Platforms, and Design-Automation Challenges Fei Su, Student Member, IEEE, Krishnendu Chakrabarty, Senior Member, IEEE, and Richard B. Fair, Fellow, IEEE Abstract—Microfluidics-based biochips are soon expected to lactate assays), deoxyribonucleic acid (DNA) analysis [e.g., revolutionize clinical diagnosis, deoxyribonucleic acid (DNA) se- polymerase chain reaction (PCR) and nucleic-acid sequence quencing, and other laboratory procedures involving molecular analysis], proteomic analysis involving proteins and peptides, biology. In contrast to continuous-flow systems that rely on per- manently etched microchannels, micropumps, and microvalves, immunoassays, and toxicity monitoring. An emerging applica- digital microfluidics offers a scalable system architecture and tion area for microfluidics-based biochips is clinical diagnos- dynamic reconfigurability; groups of unit cells in a microfluidics tics, especially immediate point-of-care diagnosis of diseases array can be reconfigured to change their functionality during [5], [6]. Microfluidics can also be used for countering bioter- the concurrent execution of a set of bioassays. As more bioassays rorism threats [7], [8]. Microfluidics-based devices, capable of are executed concurrently on a biochip, system integration and design complexity are expected to increase dramatically. This continuous sampling and real-time testing of air/water samples paper presents an overview of an integrated system-level design for biochemical toxins and other dangerous pathogens, can methodology that attempts to address key issues in the synthesis, serve as an always-on “bio-smoke alarm” for early warning. testing and reconfiguration of digital microfluidics-based biochips. The first generation of microfluidic biochips contained per- Different actuation mechanisms for microfluidics-based biochips, manently etched micropumps, microvalves, and microchannels, and associated design-automation trends and challenges are also discussed. The proposed top-down design-automation approach and their operation was based on the principle of continuous is expected to relieve biochip users from the burden of manual fluid flow [3], [4]. A promising alternative is to manipulate optimization of bioassays, time-consuming hardware design, and liquids as discrete droplets [9], [10]. Following the analogy of costly testing and maintenance procedures, and it will facilitate microelectronics, this novel approach is referred to as “digital the integration of fluidic components with a microelectronic com- microfluidics.” In contrast to continuous-flow biochips, digital ponent in next-generation systems-on-chips (SOCs). microfluidics-based biochips, which we also refer to as second- Index Terms—Biochips, design automation, microfluidics, generation biochips, offer scalable system architecture based on reconfiguration, synthesis, testing. a two-dimensional (2-D) microfluidic array of identical basic unit cells. Moreover, because each droplet can be controlled independently, these “digital” systems also have dynamic re- I. INTRODUCTION configurability, whereby groups of unit cells in a microfluidic ICROFLUIDICS-BASED biochips for biochemical array can be reconfigured to change their functionality during M analysis are receiving much attention nowadays [1]–[4]. the concurrent execution of a set of bioassays. The advantages These composite microsystems, also known as lab-on-a-chip of scalability and reconfigurability make digital microfluidic or bio-microelectromechanical system (MEMS), offer a num- biochips a promising platform for massively parallel DNA ber of advantages over conventional laboratory procedures. analysis, automated drug discovery, and real-time biomolecular They automate highly repetitive laboratory tasks by replacing detection. cumbersome equipment with miniaturized and integrated sys- As the use of digital microfluidics-based biochips increases, tems, and they enable the handling of small amounts, e.g., their complexity is expected to become significant due to the micro- and nanoliters, of fluids. Thus, they are able to provide need for multiple and concurrent assays on the chip, as well ultrasensitive detection at significantly lower costs per assay as more sophisticated control for resource management. Time- than traditional methods, and in a significantly smaller amount to-market and fault tolerance are also expected to emerge of laboratory space. as design considerations. As a result, current full-custom de- Advances in microfluidics technology offer exciting possi- sign techniques will not scale well for larger designs. There bilities in the realm of enzymatic analysis (e.g., glucose and is a pressing need to deliver the same level of computer- aided design (CAD) support to the biochip designer that the semiconductor industry now takes for granted. Moreover, it is Manuscript received February 23, 2005; revised May 16, 2005. This work was supported by the National Science Foundation under Grant IIS-0312352. expected that these microfluidic biochips will be integrated with This paper was recommended by Associate Editor J. Zeng. microelectronic components in next-generation system-on-chip The authors are with the Department of Electrical and Computer Engi- (SOC) designs. The 2003 International Technology Roadmap neering, Duke University, Durham, NC 27708 USA (e-mail: [email protected]; [email protected]; [email protected]). for Semiconductors (ITRS) clearly identifies the integration of Digital Object Identifier 10.1109/TCAD.2005.855956 electrochemical and electrobiological techniques as one of the 0278-0070/$20.00 © 2006 IEEE 212 IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS, VOL. 25, NO. 2, FEBRUARY 2006 system-level design challenges that will be faced beyond 2009, the design-automation tools. Therefore, these tools will reduce when feature sizes shrink below 50 nm [11]. human effort and enable high-volume production. As digital microfluidics-based biochips become widespread The organization of the remainder of the paper is as follows. in safety-critical biochemical applications, the reliability of Section II reviews biochip and microfluidics technology. Differ- these systems will emerge as a critical performance parameter. ent actuation mechanisms for microfluidics-based biochips are These systems need to be tested adequately not only after discussed. We also present an overview of digital microfluidic fabrication, but also continuously during in-field operation. For biochips based on electrowetting. Next, Section III discusses instance, for detectors monitoring for dangerous pathogens in design trends and challenges for digital microfluidics-based critical locations such as airports, field testing is critical to biochips. After reviewing today’s design techniques, we pro- ensure low false-positive and false-negative detection rates. pose a top-down design methodology for digital microfluidic In such cases, concurrent testing, which allows testing and biochips. This methodology encompasses synthesis, testing, normal bioassays to run simultaneously on a microfluidic sys- and reconfiguration. Challenges in the proposed system-level tem, can play an important role. It consequently facilitates design method are also identified and discussed. Finally, con- built-in self-test (BIST) of digital microfluidic biochips and clusions are drawn in Section IV. makes them less dependent on costly manual maintenance on a regular basis. Therefore, there exists a need for efficient testing II. BIOCHIP AND MICROFLUIDICS TECHNOLOGY methodologies for these microsystems. Due to the underlying A. Biochips mixed technology and multiple energy domains, the microflu- idic biochip exhibits unique failure mechanisms and defects. Early biochips were based on the concept of a DNA microar- In fact, the ITRS 2003 document recognizes the need for new ray, which is a piece of glass, plastic, or silicon substrate on test methods for disruptive device technologies that underlie which pieces of DNA have been affixed in a microscopic array. microelectromechanical systems and sensors, and highlights it Scientists use such chips to screen a biological sample simul- as one of the five difficult test challenges beyond 2009 [11]. taneously for the presence of many genetic sequences at once. The reconfigurability inherent in digital microfluidic bio- The affixed DNA segments are known as probes. Thousands of chips can be utilized to achieve longer system lifetime through identical probe molecules are affixed at each point in the array on-line reconfiguration to avoid operational faults. It can also to make the chips effective detectors. The flowchart of DNA be used to increase production yield through production-time microarray production and operation is shown in Fig. 1. Note reconfiguration to bypass manufacturing faults. System relia- that sample preparation need to be carried out off chip. There bility motivates the need for on-line reconfiguration techniques are a number of commercial microarrays available in the market to tolerate faults during field operation. Reconfiguration is also place such as GeneChip DNAarray from Affymetrix, DNA useful for yield enhancement because it can be used to tolerate microarray from Infineon AG, or NanoChip microarray from manufacturing faults. In this scenario, we assume that a mi- Nanogen [12]–[14]. Similar to a DNA microarray, a protein crofluidic biochip has been